Transcript Protein Secondary Structure Lecture 2/19/2003 Three Dimensional Protein Structures Confirmation: Spatial arrangement of atoms that depend on bonds and bond rotations. Proteins can change.

Protein Secondary Structure
Lecture 2/19/2003
Three Dimensional Protein Structures
Confirmation: Spatial arrangement of atoms that
depend on bonds and bond rotations.
Proteins can change conformation, however, most
proteins have a stable “native” conformation.
The native protein is folded through weak
interactions:
a) hydrophobic interaction
b) Hydrogen bonds
c) Ionic bonds
d) Van der Waals attractions
A Denatured protein is unfolded, random dangling, and
often precipitated (cooking egg whites).
The Native conformation is dictated by its amino acid
sequence.
 primary structure is everything.
A one dimensional strand of DNA contains four dimensional data:
height
width
depth
life span!!
The Amide bond
Linus Pauling and Corey determined the structure of the peptide
bond by X-ray.
O
OC
N
C
+
N
H
40% double bond character. The amide bond or peptide bond
C-N bond is 0.13A shorter than C-N bond. The carbonyl
bond is .02 A longer then those for ketones and aldehydes
Resonance gives 85 kJ•mole-1 stability when bond is planar!!
Peptide bonds are planar
Resonance energy depends on bond angle: 180 is max angle  cis
or trans peptide bond.
Most peptide bonds are trans, 10% that follow proline may be cis
Note: differences between bond angles and bond lengths comparing
cis and trans forms.
Torsion angles
Rotation or dihedral angles
C-N
C-C


phi
psi
When a peptide chain is fully extended the angles are defined as
180 or -180.
At 180 one gets a staggered conformation. (all trans) i.e. ethane
Note: alternating C=O pointing in opposite directions.
When viewed down the N
to C terminus axis, rotation
to the right or clock wise
increases the angle of
rotation.
Must start with the fully
extended form which is
defined as 180o or -180o
Note: this picture and the one in the book
is not correct!! The Y angle should go
the the other direction
Start with fully extended
protein structure
Rotate counter
clockwise start at +180o
and decrease angle
Rotate
clockwise start
at -180o and
increase angle
This is C-carbonyl bond or psi angle, Y
Ethane can exist as staggered or eclipsed conformation
Staggered
eclipsed
There is a 12 kJ•mole-1 penalty in energy for an eclipsed
geometry
Bulky amino acid side chains have a much higher energy penalty.
There are a few favored geometries which the protein backbone can fold
If all  +  angles are defined
then the backbone structure of a
protein will be known!! These
angles allow a method to
describe the protein’s structure
and all backbone atoms can be
placed in a 3d grid with an x, y, z
coordinate.
Ramachandran plot
If you plot  on the y axis and  on the x axis, you
will plot all possible combinations of , .
This plot shows which angles are allowed or which angles are
sterically hindered for poly-l-alanine
Secondary structure can be defined by  and 
angles
F
Y
-57
-47
 sheet
-119
113
  sheet
-139
135
310 helix
-49
-26
collagen
-51
153
 helix rt handed
Repeating local protein structure
determined by hydrogen bonding
12 proteins except for Gly and Pro
helices and pleated sheets.
Steric hindrance between the amide
nitrogen and the carbonyl
F = -60o and Y = 30o